|
Software - Protégé
|
Protégé is a free, open source ontology editor and knowledge-base framework, developed by Stanford Medical Informatics at the Stanford University School of Medicine It supports Frames, XML Schema, RDF(S) and OWL. In the PLCS comunity, it is used for the development of Reference Data OWL ontologies.
The March 2004 initial publication of the PLCS Reference Data used Protégé 2.1 Beta Build 176 and OWL Plug-in Build 97. The development of Protégé and the OWL Plug-in continues so care should be taken to test any newer releases before committing to their use for Reference Data development.
Protégé can be downloaded from (http://protege.stanford.edu/)
Download before starting (see URL's at end of page MISSING!)
Please review FAQ and user guides for more details.
Protégé is available from the Stanford University Web site. Please download the version appropriate to your computer operating system. For PLCS DEX Reference Data development, please use version 3.0(http://protege.stanford.edu/download.html) or newer. As the PLCS reference data is developed using OWL, you will require the full version of Protégé that includes the base system and optional plug-ins. This will automatically include the required OWL plug-in.
Note that if you don't already have a Java Virtual Machine (JVM) installed, you should download one. The Sun and IBM Web sites have downloads available. Protégé also has a download that comes bundled with a JVM. In order to operate Protégé you only need the Java Runtime Environment (JRE), not the full System Developers Kit (SDK).
Once the JVM/JRE is ready, install Protégé as directed. Note that you can test by verifying JRE is available to system (Windows: Use Control Panel) if you are unsure.
Install Protégé using all defaults. Choose the JRE you just installed or that already existed (remember only 1.4.2 or 1.4.3 work as of April 2004). During installation you will be asked which components of Protégé to include. Select "Everything" to ensure that the OWL plug-ins are installed.
Test by starting and opening test "newspaper" ontology.
Test the OWL plug-in by creating new "OWL Files" Ontology.
To enable Protégé to use local OWL files, rather than those found on the Web, you need to update the ont-policy.rdf file provided as part of the OWL Plug-in. An example is provided in dexlib. Before setting this up, please compare the downloaded ont-policy.rdf in the OWL Plugin folder to see if it has changed. If so, add the plcs and Dublin Core elements from the PLCS version of this file to the new one. Over time, the ont-policy.rdf file is likely to change as the Protégé OWL Plugin is developed.
You should copy dexlib/data/refdata/ont-policy.rdf wherever you have installed Protégé OWL plug-in (e.g: Protege_3.0/plugins/edu.stanford.smi.protegex.owl/ont-policy.rdf).
Edit that file so that the ENTITY plcs points to the folder where you have installed the dexlib/data/refdata folder in dexlib.
EXAMPLE <!ENTITY plcs 'file:///d:/rbn/projects/nist_module_repo/dexlib/data/refdata/'>
The OntologySpec element in the ont-policy.rdf file specifies the natural URI you'll put in your data, the alternative location (e.g. your dexlib folders), the type of the file which is OWL in our case, and the XML namespace prefix to use. Note that this prefix must match exactly the XML namespace used in the OWL files making up the Reference Data.
This capability allows you to specify the final, proper URI during the development of the Reference Data. When finally published on the Web without the use of the ont-policy.rdf redirection, the Web addresses will be correct.
If you want to use OWL files directly from the Web, then do not include them in the ont-policy.rdf file.
This section explains how to use the Protégé tool to specify various aspects of the PLCS Reference Data.
create a Necessary & Sufficient Condition and define that a Superclass is made up of a union of subclasses. In Protégé:
you add a disjoint statement for each subclass. In Protégé:
The OWL Language has the built in capability to state that two classes have exactly the same members. From the OWL Web Ontology Language Guide : The property owl:equivalentClass is used to indicate that two classes have precisely the same instances. Note that in OWL DL, classes simply denote sets of individuals, and are not individuals themselves. See Section 3.2.2 of the OWL Web Ontology Language Reference (http://www.w3.org/TR/owl-ref/#equivalentClass-def).
The OWL Language also has the built in capability to state that one class is defined as the unionOf, intersectionOf or complementOf of other classes. For the creation of PLCS Reference Data, this set theory capability of OWL is included in OWL DL and so may be used. See Section 3.1.3 of the OWL Web Ontology Language Reference(http://www.w3.org/TR/owl-ref/#Boolean)
Class equivalence can be created in Protege by:
An example screen shot of Protege is shown in Figure 3.
The resulting OWL is:
<owl:Class rdf:ID="y">
<owl:equivalentClass>
<owl:Class rdf:ID="x"/>
</owl:equivalentClass>
</owl:Class>
<owl:Class rdf:about="#x">
<owl:equivalentClass rdf:resource="#y"/>
</owl:Class>
This section has not yet been reviewed or agreed.
This section has not yet been reviewed or agreed.
This section has not yet been reviewed or agreed.
Who uses the class - which organization has contracted against an ontology or a subset of the ontologies?
This section has not yet been reviewed or agreed.
We may need to identify the reference data...
This section has not yet been reviewed or agreed.
This section has not yet been reviewed or agreed.
The PLCS information model is represented by converting the EXPRESS entities to OWL classes - EXPRESS/OWL classes. Reference data is generated by creating sub classes of these OWL classes.
This section has not yet been reviewed or agreed.
There is some reference data that is used to provide additional semantics to the PLCS information model or to clarify the ambiguity of the model. This reference data is typically used where the PLCS model is inadequate, but was not be modified in order to preserve compatibility with existing parts of the STEP standard.
This section has not yet been reviewed or agreed.
Qualifier classes are used to qualify an assignment. For example, a typical or actual date is represented by qualifying a Date_or_date_time_assignment as being typical or actual.
The application of a qualifier class is achieved by making the EXPRESS entity to which the qualifier applies a sub class. An example is shown in Figure 2.
This section has not yet been reviewed or agreed.
The majority of OWL classes are classes particular to a given domain.
This section has not yet been reviewed or agreed.
During the development of the capabilities, some reference data is used as examples in the text describing the capability. Rather than including this reference data in the standard set of reference data to be published, it is stored in a separate OWL file plcs-rdl-examples.owl(../../data/refdata/plcs-rdl-examples.owl).
The Protégé Ontology Editor and Knowledge Acquisition System (http://protege.stanford.edu/)
Protégé FAQ(http://protege.stanford.edu/faq.html)
OWL Plugin FAQ(http://protege.stanford.edu/plugins/owl/protege-owl-faq.html)